It's all in the details
by bubblegirl89236
Summary: Memories make the man. So what is the man without the memories? John is losing his mind piece by piece, will someone be able to put it back together before there is nothing left of the man they once knew. Image courtesy of 'dream designs' from FreeDigitalPhotos .net
1. Chapter 1

**My first Atlantis Story upload.**

**This story is almost complete on my computer (just a little in the middle to do, ironically the details that are important to the rest of the story).**

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><p>Set on June 27th 2008<p>

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><p>John was doing some laps around the city, listening to some music as he went, radio in his pocket.<p>

Ronan was waiting for him at the end of the corridor and John jogged over putting away his headphones and attaching his radio.

"Hey bud, what's up?" John said using a towel he had waiting for him to wipe his face then draping it over his shoulder.

"You said you were meeting us for lunch...that was two hours ago Sheppard" Ronan said.

John looked at his watch to check, "crap, I forgot. I _am _feeling hungry... Fancy seconds?" John said not wanting to eat on his own if he could help it.

"Sure" Ronan said shrugging.

~Cafeteria~

John and Ronan finished their respective meals and sat back and relaxed for a bit. Putting their feet up on some spare chairs.

"So where is everyone else? They not hungry" John said.

"Sheppard, you ok?"

"Yeah, why?"

"You missed lunch, remember?"

John stood up and his legs almost buckled, luckily he used his reflex grip on the table to steady himself.

"I think I should take you to the infirmary" Ronan said.

"Maybe that's a good idea" John said really confused.

~Infirmary~

"What did ya do to each other this time?" Carson said looking for any obvious signs of injury.

"There's something wrong with his memory" Ronan said.

"And my legs, it feels like i've been running for hours"

"You have" Ronan said.

"Oh" John said promptly shutting up and allowing Carson to direct him towards the scanner.

~An hour or so later~

"What's going on?" Rodney asked upon seeing Teyla and Ronan already seated beside John.

"We do not know, Dr Beckett is running some tests" Teyla said, clearly concerned with his condition.

"Sheppard" Rodney said giving John a small push, trying to see his condition for himself.

"Dr Beckett gave him something to make him sleep. He was confused and wouldn't allow Carson to run his tests...It was either that or restraints"

"Carson what is it? I've seen that look, how bad is it?" Rodney said, seeing Carson reviewing the results of John's scan.

They all crowded around the doctor hoping that this thing was reversible.

"What look? Anyway do ye see these?" Beckett said pointing to a section in John's brain.

"Is that what I think it is?" Rodney asked hoping that for once he was wrong.

"Yes and no" He replied.

"What? They either are nanites or they aren't" Rodney said confused.

"They're not nanites, but they do appear to be be similiar in design. These are much smaller and are most concentrated in his brain, currently affecting the short term memories but it's progressive, they seem to be increasing in number but there is no visible evidence of replication"

"What about an EM pulse? If these are earlier models surely that should work" Rodney said.

"I'm not sure what the effect on the Colonel's brain this would have. I don't want to risk brain damage"

"Where did they come from? And why isn't any one else having memory problems?" Ronan asked.

"Dr Beckett" Dr Keller stammered.

"What is it?" he said turning to see the worried look on her face.

"You better come see this" she said calling up the data onto the screen.

"This is the Colonel's blood sample, you can see them here. Now watch" she said.

"Where did they go?" Rodney asked as the little machines dissapeared.

"I took some random samples and most of them are clean the ones that aren't the same thing happened and I called them in for a follow up scan and blood test and they were completely clean...Since these do not seem to self replicate I can only come to the conclusion that they must be targetting Colonel Sheppard. I should run some more blood tests just to be sure that he is the only target"

"One of the ancient labs playing up again McKay?" John said coming around.

"Erm, no, well I don't think so" Rodney said not knowing of any at this time.

"What's going on?" John said sitting up.

Apart from an ache in his legs he felt fine.

"What's the last thing you remember?" Carson asked.

"Sparring with Ronan. Did you hit me?" John asked.

"What's the date?" Rodney said wanting a more accurate answer.

"12th April" John replied.

"That's not too bad" Rodney said.

"And the year?" Carson said.

"2007. Did I hit my head or something?" he said with no hesitation.

There was silence, no one knew how to tell him that he was slowly losing his mind. Although the silence in itself told John that this was more serious than a concussion.

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><p><strong>AN - And there's the best point I thought I could end the chapter.**

**What is a man without any memories? ... An empty shell.**


	2. Chapter 2

**Next chapter up.**

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><p>"John it's the 27th of June 2008...you've been infected with microscopic robots that are affecting your memory" Carson said as gently as possible.<p>

"nanites?" he said thinking that they were doging that word.

"no, these are more like an earlier less effective form. They're increasing in number but they aren't replicating. If we can't find out where they are coming from then your memory loss is going to increase until.."

"Anything youffok can do for me here?" John said cutting Carson off whilst maintaining his composure.

"No but..."

"Then no offence Doc but I want to get out of here, whilst I can" John said knowing that one way or another he was getting out of the infirmary.

"He will not be alone" Teyla said seeing that Carson was not completely convinced that it was a good idea.

"Alright, but I want to be kept informed of his progression" Carson said not wanting to keep him in the infirmary as with the memory loss it might get to the point that he would have to be restrained if he learned that he was not able to leave.

More than anything John wanted to be alone in his quarters, but in hiss current state of mind had to comprimise and ended up in his room with one of his friends watching him like a hawk, each taking shifts.

Except for Rodney, after finding out that something similiar to nanites was behind it he was beginning to think the colonel was right after all maybe this was because of some device inside the city. At least that way there was a chance of finding whatever was causing this and reversing it.

~Teyla~

John was lying on his well made bed staring at the ceiling, giving no insight to how he was coping with all this.

Teyla was concerned by not being able to tell what was going through his mind.

"I'm fine" John said without taking his eyes off the ceiling.

"I know you John, staying cooped up in your room is not like you, even given the circumstance"

"Knowing that there's nothing I can physically do is killing me. I know it's going to get to the point where I don't recognise any of you or even where I am, I won't be me anymore. At least I won't know that..."

"We have not given up on you John, you should not give up on us. Rodney is scouring the city looking for something that could have done this to you. It is more than understandable for you to be scared, but sulking in your room..."

John stood up clearly not wanting to give her the satisfaction of being right.

"Fancy sparring with me, whilst I remember how to fight" he asked, knowing that she would never refuse.

She gave a nod and the two made their way over to the gym.

Even after loosing a year of his memory, he was still holding his own, probably taking out some aggression towards the situation and from the scolding he took from Teyla. He still ended up on his ass but it was not an easy task on her part. She dared not to take it easy on him, he would most certainly take offence.

By the time it came to a switch over they were both out of breath and ready to call it quits.

*Ronan*

Teyla had to go and put Torren down to sleep.

They were relatively silent throughout eating their respective meals, but that was normal for the two of them. They went through so much together that it left hardly anything left unsaid.

Ronan was glad Teyla had snapped John out of it and allowed him to act like himself whilst he could. Ronan was like John in the sense that they never really talked about what was really going on with them when it mattered, but Teyla had this way of cracking them open.

John himself seemed a bit more at ease with things given that he wasn't being treated any differently by the people that mattered to him the most. Making the most of what time he had left before another piece of him had left he decided to behave just like he would normally.

"Since you know I'm losing my mind and all, any chance you'll tell me where you got your gun from?" John said eying up the blaster whilst simultaneously taking his mind off his troubles.

"Nice try Sheppard"

"Damn, was worth a shot. I really really want one of those. Guess I'll have to get McKay to build me a better one..." John pouted.

"You can try"

Teyla joined them at the table.

"Are you ok?" John asked seeing Teyla look exhausted.

"Yes, thank you. Torren was fighting his sleep" Teyla explained.

"he is my son" she said seeing the confusion on his face at the mention of the new name.

She mentally kicked herself, she had forgotten what it was like for Torren not to be around and it had slipped her mind.

"Why do you do those?" Ronan asked watching John doing some sudoku puzzles as Teyla ate.

"It keeps my mind busy" John said keeping his eyes focused on the page.

"I always hated math" Ronan said.

"It's not math...it's more like a puzzle" John said not wanting to be classed as a geek.

"Whatever" Ronan said taunting him.

"I think I'm going to the infirmary and grab some tylenol, I have one hell of a headache"

"It's about time for your check in anyway" Teyla said, finished with her meal.

John went to look at his watch but found his left wrist bare.

"your watch had the date" Ronan explained.

*Infirmary*

Carson had ushered the others out of the infirmary so John could get some sleep. He was to be monitered so that he didn't freak out and do something stupid.

Other than John's deteriorating memory he was in fine physical condition so he was only hooked up to a heart monitor just as a precaution, especially as the machines were working at a microscopic level and could cause a whole heap of trouble"

John had shut the curtains to give himself some privacy.

Carson went to check on the Colonel before he turned in for the night. He drew back the curtain to find the bed empty; the heart monitor unconnected at the wall.

"Rodney are you awake?" Carson said over his radio.

_"Yes. What is it? Is Sheppard ok?" Rodney said stopping what he was doing._

"He's left the infirmary. Any chance you can track down his transmitter signal"

_"Of course I can. He's on a pier in the section that's just been cleaned up"_

~John~

John had managed to move through the city unnoticed. It helped that there was no imminent threat looming over Atlantis so most of the corridors were empty at this time of night.

It was not clear even to John himself if he had left the infirmary on purpose or merely forgotten as at this point he had no recollection of how he had gotten there.

Rodney told Ronan and Teyla of the situation and since they were closer to John's location they went to get him.

Carson remained on standby, in the event John was hurt, he would be ready.

Teyla approached John first, "John. What are you doing here?" Teyla asked, noticing how cold it was out here.

John was lying on the ground looking up at the stars.

"I know I'm losing time, I don't even remember how I got here, I guess I just needed to be alone"

"Time to go back buddy" Ronan said extending his arm.

John grabbed his arm and allowed Ronan to help him to his feet.

Walking back to the infirmary, John began to slow until he came to a complete stop and fell to his knees cradling his head.

"John!" Teyla said, voice filled with concern

"Just a headache" he said, concerned by the fact that it had brought him to his knees.

"Let's get you to the infirmary" Ronan said hauling him to his feet, allowing John to hold on to him until he got his footing.

They began to get back to their usual pace, John hanging back to be next to Teyla.

"Who is this guy?" John whispered.

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><p><strong>John is losing his grip on the world...<strong>


	3. Chapter 3

**Next chapter up. Sorry for the short delay - was dealing with university stuff.**

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><p>*Rodney+Zelenka*<p>

"Aha got it" Rodney said typing away.

"Remember when one of the unexplored ancient labs suffered a huge powersurge a while back, it fried the database in that section. It took me a while but I've put enough of it back together again. The machines that infected Sheppard were actually build after the ancients had tried destroying the replicators, and are strictly for medical purposes" Rodney explained.

"Clearly they still need a bit of work" Radek said.

"Actually no they don't. They can't work properly on their own, they work in conjunction with a machine in the lab that instructs them on what to do before removing them. I guess the ancients learned from their mistakes for once"

"But then why target Sheppard"

"My best guess is because, as much as I hate to say it, out of all of us, he is the closest we have to an ancient and they were designed for ancients"

"Will it restore his memory?"

"It should if it works correctly" Rodney said trying to ignore the Ancient's track record with failed experiments.

"We better hurry, Colonel Sheppard does not have much time"

"I know" Rodney whispered, not really appreciating the reminder.

*Infirmary*

"What happened this time? Elizabeth is going to have a field day" John said.

He was met with silence and sad eyes.

"What am I dying? Did anyone else get hurt?" John said thoughts running through his head a mile a minute.

They had been discussing what they should and should not tell him. At this point they saw no good reason to give him bad news if they could avoid it, it would only agitate him, and he would forget shortly.

"You are having memory problems. Rodney thinks he has found a solution and is working as fast as he can" Teyla said.

"If it's just my memory why am I in the infirmary?"

"Because if it gets any worse, you won't know where you are. And it caused you to pass out"

"and the headaches?"

"Aye. The painkillers seem to be having no effect" Carson said.

*Ancient Lab*

Things were moving fast, just not as fast as any of them would have liked. John's condition was deteriorating rapidly and if they didn't hurry up Carson was pretty sure that John's body would begin to shut down.

"Need a hand?" Sam said entering the room.

"We could definitely use an extra set of hands. How are you with ancient systems?" Rodney said appearing from behind the console.

"Not too bad actually, I've been familiarizing myself with them in my spare time. We can't always wait around for the great Rodney McKay" she said giving his ego a good rub.

"I could really use you over here" Rodney said disappearing back behind the console. They needed the console to be in full working order so that they could instruct the machines to repair any damage they have caused.

*Infirmary*

"Do I know her? Cause she is hot" John said after Teyla had left him with Ronan.

"She's on your team"

"Wow this is so cool. My life is awsome!" John exclaimed.

Ronan smirked in response, even though John had the mental age of a late teen, he was still John.

"McKay will fix you up"

"hey-y nice gun, do we all have those?"

Before Ronan could respond John started to rub his forehead with his finger tips.

"Headache?" Ronan asked.

"my head feels like its going to explode" John ground out.

Dr Beckett heard all the commotion and came over.

"All I can do is give him a sedative" Carson explained to Ronan as John was a little pre-occupied.

"Do it" Ronan said, wondering if John's high-threshold for pain still applied.

"it'll take a few minutes to kick in" Carson said.

John put his hands down and waited for the medication to kick in.

His eyes rolled up and he fell back to the bed and started to convulse...

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><p><strong>AN - will re-edit soon after completion as there are some things I am not completely happy with**


	4. Chapter 4

**Final Chapter**

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><p>Carson had seen this coming, but had hoped that Rodney would have got the machine up and running first. The machines were causing all kinds of trouble inside the Colonel's brain, now including causing seizures. Throughout the night he had suffered three more seizures, each time causing him to get weaker, he would not be able to take much more. The picites (as dubbed by Rodney due to the fact they were roughly one picometer in size) were systematically blocking the memory pathways and causing the very problems they were designed to prevent.<p>

"McKay better hurry up, he's not going to last much longer" Ronan said.

"From what I understand he is almost ready" Teyla said.

"Can't we just put him into stasis?" Ronan queried.

"His body can't take the strain of it at this point, and God knows how the machines will react" Carson said joining them at the end of the bed.

"How are you feeling?" Teyla asked John as he returned to the land of the living.

"My head hurts. When can I go home?" he asked innocently, the lack of trying to insist he was fine concerning everyone.

"As soon as we fix you" Teyla said giving his shoulder a reassuring squeeze.

"ok...will you stay with me?" he said looking away sheepishly.

"of course I will John" she smiled.

By now John had the mental age of a three year old...literally.

She had given John a pencil and a sketchbook to keep him from being bored.

When she had returned about an hour later he was asleep, head next to his book on the table.

She was curious to see what he had drawn. As it turns out he had filled the sketchbook in this short time and could draw exceptionally well apparently from even the age of three.

"I'm sorry to disturb you John, but it's time" She said gently shaking him awake.

"John, wake up" she said louder; but she recieved no response, not even a twitch.

"Carson, I cannot wake him" she explained her concern laced in her voice.

"We're running out of time" Carson said checking the monitors.

Dr Beckett and Teyla rolled the bed down to the lab using a transporter or two along the way, escorted by a small medical team in the event something else went wrong.

Carson had one of the male nurses assist him with transferring John to the examination table.

Rodney remained shockingly silent at the sight of John this still, he pushed the faceplate until it was half an inch above John's face.

The system automatically scanned for the picites and showed them on the display screen, which was now McKay's laptop.

"They're not just in the memory regions of the brain. They are in the hyperthalamus too, that's why we can't wake him up" Carson said.

"Is the programme ready?" Teyla said.

"er, yes of course" Rodney said snapping out of it.

Rodney typed away into his laptop and started the programme.

The faceplate lit up and the picites began to dissapear from the screen, slowly but surely.

Once they were more or less out of the hyperthalamus John's eyes snapped open, his pupils blown and unfocused.

"No!" John said struggling to get out but the others were keeping him down.

"What do you mean no? We're trying to help you" Rodney said, monitoring the machine as if it broke during the programme they would lose John for good.

"No more scans, I don't like it, they promised" John said reliving some early memories.

Teyla indicated for Rodney to finish.

"They said I, I , I could see her one more time" he whispered until he began to hear a soft voice whispering his name as he passed out allowing everyone else to remove their grip.

The power output of the device began to spike causing John's back to arch and his unconscious body to spasm uncontrollably.

"Rodney, shut it off" Carson ordered.

"I'm trying..." Rodney said tapping away on his computer.

The console shut off and John's body went lax.

"The buffer is empty.." Rodney said with mixed emotions.

"That's good right?" Ronan asked.

"All we can do is wait and see" Rodney said frowning contemplating what the consequences would be if the John they knew was truly lost...

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><p><strong>People with memory loss sometimes recover on their own but when something like this is at work it's just not that simple. Will John become an echo of what he was before and start again; a blank slate? The people of the pegasus galaxy better hope not.<strong>


	5. Chapter 5

A/N** - I apologize for the confusion that I had left this story incomplete - I didn't really think of an Epilogue as an actual chapter (since then I have fleshed it out a bit more - the rest of the revamp coming soon), but at least some of you should be surprised. The final FINAL chapter!**

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><p>The faceplate lifted upon completion of the programme. And the machine powered itself down.<p>

John's head lolled to the side, Carson quickly checked his pupil responsiveness with his penlight.

"We have to get him back to the infirmary now" Carson said.

"What is it?" Rodney asked.

"He's slipped into a coma..." Carson sighed, leaving the room, trailing Sheppard.

***A week later***

"Any change?" Rodney asked Carson making his second visit to the infirmary today; hoping that John had woken from his coma.

Carson shook his head, "It's not your fault Rodney, maybe he just needs some more time, you didn't really think he would bounce back straight away did you?"

"No, but it's Sheppard, you know? Since when has anything kept him down?"

"Aye, I've never met anyone quite like him. But don't count him out just yet" Carson said as Rodney had a quick look to reassure himself.

"Did you move him?" Rodney said after taking a quick peek through the privicy curtains.

Carson threw open the curtains to reveal an empty bed, the sheets askew and various tubes on the floor.

"Colonell Sheppard is no longer in the infirmary" Carson said over his radio.

_"I've notified Teyla and Ronan, they are on their way" Chuck said knowing that an unarmed runaway patient was not a good reason to start a city wide man hunt, even if the man in question was John Sheppard._

"Did he wake up?" Rodney said trying to contain his hope.

"No one saw him leave, let alone wake up" Carson said after conferring with the nurses currently on shift.

Most people were asleep at this time of night or needed on their posts which ruled out very few places that he could have gone to.

Ronan and Teyla ran in.

"We'll track him down" Ronan said turning immediately to McKay.

"I'll just go get my...computer" Rodney said pausing when Ronan, after taking the initiative, held up his laptop.

Rodney brought up the relevant programme and selected the frequency of John's transmitter, "He's heading towards the south pier" Rodney said closing his laptop so he could catch up with Ronan and Teyla who had bolted the moment they had heard pier.

They found John lying on the floor in black medical scrubs, eyes staring at the stars in the night sky, with no shoes and it was freezing out here in the middle of the night.

"What are you doing out here buddy?" Ronan asked as gently as a man his size could.

"I don't know" he said keeping his gaze fixed on the sky.

"Let's get you inside before you get sick" Teyla said draping a blanket around him.

"Thanks. Where exactly are we anyway? And where are my shoes?" he said standing up, suddenly aware of the temperature.

They all stopped dead and looked at each other.

"What is it?"

"What's the last thing you remember?"

"Waking up in the infirmary"

"And before that?" Rodney pushed.

John thought about it and drew a blank.

"Let's get you back to the infirmary" Ronan said wanting an actuall report from Carson as they did not want to have to chase him through the city if he didn't like what he heard.

"So..." Ronan said reading Carson's facial expression.

"So, he's not quite the man we remember, but I'm certain he's in there somewhere, right now he knows the basics, but people and relationships are a complete mystery to him at the moment. Show him any photos you have of him with you try and jog his memory and the gaps might dissipaite. He has to want to remember or he may never recover his memory"

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><p><strong>*John's*POV*<strong>

"So you remember Atlantis?" Carson asked.

"Yeah, it's hard to forget when you've linked your mind to the city"

"Can you remember how to fly?" Rodney said hoping that the mental componant that links him to Atlantis would be the same for the jumper.

John threw him a confused look, thinking he was trying to get him to jump out a window or something.

"Come on, you'll love it"

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><p>The next thing he knew he was flying the jumper in space, it felt so natural, so easy.<p>

"Think it's time for us to go back" Rodney said.

"Are you able to fly this?"

"Yes, although not as good as you"

"Maybe I'll give you a lesson some time"

"That would..."

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><p>"What is this?" John said finding himself sitting next to Teyla who had some things to give to him.<p>

"Dr Beckett said pictures should jog your memory, we have shown you all the photographs we have but I thought you should see what you hung on to the longest" She said handing him a sketchbook.

"I drew all these?" he asked.

"Yes, you seem to have a gift for drawing"

"Can I keep this?"

"Yes of course, it is yours" she said leaving him in peace to look through it.

John began to make his way to the infirmary and started flipping through the pages, there were various people inside, and a lot of ancient devices. He recognised most but he found one of a woman who he couldn't remember, but every time he looked at her face he felt sad and it made his heart ache.

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><p>Suddenly a bantos stick was heading towards him, he managed to deflect it with one in his hand out of reflex.<p>

"You ok there Sheppard?" Ronan asked noticing the change in his demenor.

"I'm fine, you just caught me off guard"

"You seem to remember how to fight"

"Must be a built in instinct, when I try to remember something I..."

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><p>John was sitting on a bed in the infirmary with his arm bandaged.<p>

He unravelled it to find a deep looking gash that has been stitched along his left forearm.

"Why did ye go and do that for?"

"What happened to my arm?"

"Don't you remember? Ronan brought you in after you cut yourself on a big piece of glass that hadn't been cleared up yet.

"I've been blacking out, doc"

"Why does it take blood for any of ye to come in here. Then I could have told you it is most likely your memories coming back, but too fast for your brain to process, but I'll run a scan just to be sure"

"Thanks Car..."

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><p>John found himself in the cafeteria with Teyla, Ronan and McKay who were telling him stories that he was involved in, in an attempt to get him to remember.<p>

"I'll never be able to forget when you kissed Dr Beckett" Lorne said causing John to choke on his drink laughing.

Everyone paused to look at him.

"What? Is there something on my face?"

"John?" Teyla probed.

"Yeahhh" John said confused with his current treatment.

"Why were you laughing?"

"I was just remembering McKay's face when he regained control...it was priceless" John said trying not to laugh at the memory...again.

"Will you guys stop looking at me like that!" John said feeling like he was missing something.

"You remember that?" Ronan asked.

"How could anyone forget that" he sniggered, wondering why McKay was defending himself.

"So you know who we all are...you know, really, really?"Rodney said not knowing how to quite phrase the question on the tip of his tongue _"Are you back?"_

"Sure your son is partially named after me Teyla, Ronan when we first met you tied us up, Meredith McKay deathly allergic to lemons" he said with a smirk that only he could do.

**_He's back alright..._**

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><p><strong>Q&amp;A time:<strong>

**Q1: How did Sheppard come into contact with the piconites?**

**Q2: What Activated them?**

**Q3: Why did they wipe Sheppards memories?**

**A: The container that held the piconites was broken during the power surge and only had rudimentary programming written into their base code. They were activated as a result of the power surge. The piconites sought out the closest being to ancient physiology on Atlantis, which is John (in my opinion he is at least half ancient on his mothers side - but that's another story...literally). By placing themselves throughout the memory regions of the brain, in preperation for repair, they block the pathways between the memories and the brain itself and store the data to make sure that the patient can make the greatest possible recovery, and they were designed to work within a day at most so memory loss was a rare side affect.**


End file.
